The -49 rectifier board uses a higher current bridge rectifier setup for the feature lamps because games using it were the first to have the auxiliary lamp driver board for extra lamps. It also resulted in there being an extra header pin (9th position) on the J1 playfield connector where as the -18 rectifier board only has an 8 position J1 pin header.

You should have no problem installing the -49 in a -18 game apart from mounting. Just make sure you install the playfield J1 connector in the proper location - the 9th pin on the right should be left exposed and unconnected.